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https://trialdesign.org/

Integrated platform for designing clinical trials.

Proper citation: Trialdesign (RRID:SCR_021749) Copy   

•   Source: SciCrunch Registry

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https://github.com/gabraham/flashpca

Software tool as fast principal component analysis of large scale genome wide data. FlashPCA performs fast principal component analysis (PCA) of single nucleotide polymorphism (SNP) data. FlashPCA2 used for principal component analysis of biobank scale genotype datasets.

Proper citation: FlashPCA (RRID:SCR_021680) Copy   

•   Source: SciCrunch Registry

https://github.com/ODonoghueLab/Aquaria

Web application to help biologists use 3D structures to gain insight into protein function. Used in revealing novel insights into molecular mechanisms underlying protein function in health and disease. System for incorporating 3D structures into variant analysis.

Proper citation: Aquaria (RRID:SCR_021834) Copy   

•   Source: SciCrunch Registry

https://doi.org/10.15252/msb.202010079

Web tool to visually summarise all available 3D structural information for all proteins comprising COVID-19 virus (SARS-CoV-2). Resource also gives access to structural models, generated by finding all sequence regions with detectable similarity to any currently published 3D structure. These structures are clustered into distinct states that provide insight into viral replication, mimicry, and hijacking.

Proper citation: Aquaria COVID Resource (RRID:SCR_021835) Copy   

•   Source: SciCrunch Registry

https://www.microns-explorer.org/

Portal to release connectivity and functional imaging data collected by consortium of laboratories led by groups at Allen Institute for Brain Science, Princeton University, and Baylor College of Medicine, with support from broad array of teams, coordinated and funded by IARPA MICrONS program. Data include large scale electron microscopy based reconstructions of cortical circuitry from mouse visual cortex, with corresponding functional imaging data from those same neurons.

Proper citation: Microns Explorer (RRID:SCR_021678) Copy   

•   Source: SciCrunch Registry

https://www.nanostring.com/products/ncounter-analysis-system/ncounter-systems-overview/

System includes hardware and software. Options include nCounter SPRINT,nCounter MAX or nCounter FLEX. Platform used for multiplex analysis of up to 800 RNA, DNA, or protein targets. System can be combined with GeoMx Digital Spatial Profiler (DSP) to enable high-plex, spatially-resolved RNA, and protein quantification.

Proper citation: NanoString: nCounter Analysis System (RRID:SCR_021712) Copy   

•   Source: SciCrunch Registry

https://github.com/benmurphybaum/StimGen

Software tool as interface for designing and presenting visual stimuli.

Proper citation: StimGen (RRID:SCR_021676) Copy   

•   Source: SciCrunch Registry

https://yaml.org

YAML is a human friendly data serialization language for all programming languages. Unicode based data serialization language designed around common native data types of agile programming languages. Useful for programming needs ranging from configuration files to Internet messaging to object persistence to data auditing.

Proper citation: YAML (RRID:SCR_021710) Copy   

•   Source: SciCrunch Registry

https://www.trikinetics.com/

System from TriKinetics for monitoring Drosophila activity. Includes hardware and DAMSystem3 Software for data acquision and DAMFileScan Software for scanning data for errors. Applied to behavioral activity experiments, including sleep deprivation analyses and general studies of hypoactivity and hyperactivity.

Proper citation: TriKinetics: Drosophila Activity Monitoring System (RRID:SCR_021798) Copy   

•   Source: SciCrunch Registry

https://pycaret.org/

Open source, low code machine learning library in Python that allows you to go from preparing your data to deploying your model within minutes in your choice of notebook environment.

Proper citation: PyCaret (RRID:SCR_021695) Copy   

•   Source: SciCrunch Registry

https://www.zeiss.com/microscopy/int/products/microscope-software/zen.html

Software package for ZEISS light microscopy systems. Universal user interface for every imaging system from ZEISS to assist to acquire images, process images, visualize big data by GPU powered 3D engine, analyze images via Machine Learning-based tools, correlate between light-light or light-electron microscopes, store raw data in secure format locally or in the cloud., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: ZEN-ZEISS Efficient Navigation (RRID:SCR_021725) Copy   

•   Source: SciCrunch Registry

http://rna.informatik.uni-freiburg.de/MutaRNA/Input.jsp

Web server predicts and visualizes mutation induced structure changes of single nucleotide polymorphism in RNA sequence. This covers changes in accessibility (single strandedness) of molecule, its intra molecular base pairing potential and its base pairing probabilities. One of Freiburg RNA tools.

Proper citation: MutaRNA (RRID:SCR_021723) Copy   

•   Source: SciCrunch Registry

https://www.nature.com/articles/nprot.2014.131

Software tool calculates direction autocorrelation, plots and calculates other essential parameters to analyze cell migration in two dimensions: it displays cell trajectories individually and collectively, and it calculates average speed and mean square displacements (MSDs) to assess the area explored by cells over time.

Proper citation: DiPer (RRID:SCR_021720) Copy   

•   Source: SciCrunch Registry

https://www.cancer.gov/about-cancer/treatment/drugs

Portal to find consumer friendly information about drugs for cancer and conditions related to cancer. The list is in alphabetical order by generic name and brand name.

Proper citation: NIH NCI list of FDA approved cancer drugs (RRID:SCR_021841) Copy   

•   Source: SciCrunch Registry

https://github.com/kukionfr/VAMPIRE_open

Software tool for analysis of cell and nuclear morphology from fluorescence or bright field images. Enables profiling and classification of cells into shape modes based on equidistant points along cell and nuclear contours. Robust method to quantify cell morphological heterogeneity.

Proper citation: VAMPIRE (RRID:SCR_021721) Copy   

•   Source: SciCrunch Registry

https://github.com/Murali-group/SARS-CoV-2-network-analysis

Software tool to predict human proteins that interact with SARS-CoV-2 proteins and trace provenance of predictions.

Proper citation: SARS-CoV-2 network analysis (RRID:SCR_021811) Copy   

•   Source: SciCrunch Registry

https://www.mayo.edu/research/labs/tissue-repair-mechanobiology/software

Software tool to calculate 2D tractions exerted by adherent cell on its substrate. Used in field of mechanobiology to study contractile responses of variety of cell types.

Proper citation: TractionsForAll (RRID:SCR_021819) Copy   

•   Source: SciCrunch Registry

https://manualzz.com/doc/6543996/drosophila-activity-monitoring-system-user-s-guide

Software tool used in Drosophila Activity Monitor system to scann data for errors. Also allows user to extract data from monitor files and bin data in different lengths.

Proper citation: Trikinetics DAM FileScan (RRID:SCR_021817) Copy   

•   Source: SciCrunch Registry

https://github.com/VisionandCognition/NHP-pycortex

Software tool as adaptation for NHP brains and pipelines. Pycortex python based toolkit for surface visualization of fMRI data.

Proper citation: NHP pycortex (RRID:SCR_021815) Copy   

•   Source: SciCrunch Registry

https://www.ebi.ac.uk/eqtl

Catalog provides uniformly processed gene expression and splicing QTLs from all available public studies on human. Expression and splicing QTLs recomputed from public datasets.

Proper citation: eQTL Catalogue (RRID:SCR_021700) Copy   

•   Source: SciCrunch Registry